ABSTRACT Global malaria elimination has little chance of success in the absence of an effective vaccine. The leading candidate vaccine (RTS,S) has shown only moderate efficacy in a completed Phase III trial but was recently given scientific support by the European Medicines Agency, allowing it to be assessed for the World Health Organization preferred medicines list as it has a potential large impact given the magnitude of malaria burden. The vaccine does not work equally well in different populations; this variability may be due to parasite, environmental, or host factors. Furthermore, any malaria vaccine will not be used in isolation, but rather as part of an integrated program leveraging other control measures. Therefore, understanding the combinations of factors which modulate the effectiveness of a malaria vaccine is essential to guide appropriate vaccine use and formulating next-generation vaccines. This proposal is designed to improve our understanding of how RTS,S works by evaluating key ecological, host, and parasite factors which likely impact effectiveness. The approaches proposed will enhance our understanding of the effectiveness of RTS,S and can also be leveraged to improve the efficacy of future malaria vaccines. Data suggest that RTS,S efficacy varies based on transmission intensity. The first goal of this proposal is to expand these findings to a larger context. We will investigate ecological and behavioral factors that may influence vaccine efficacy across three RTS,S trial sites in Malawi, Ghana, and Gabon. These data, in conjunction with Phase III trial data, geographic information system (GIS) and satellite data, and a concurrent malaria transmission intensity study, will allow us to discern the impacts of individual and neighborhood factors on vaccine effectiveness in an ?ecological? analysis of the trial. The second goal leverages the experience in the proposed team of investigators for studying antigenic diversity in malaria to understand the importance of strain-specific protection to the vaccine antigen circumsporozoite protein (CS) during the trial. Recent evidence has shown strain selection by the vaccine, with a higher level of vaccine efficacy against vaccine type CS strains. However, the longevity of strain specific immunity is not known. If immunity to vaccine type strain is longer-lasting than to non-vaccine type strains, this has important implications for vaccine design and suggests the need for a polyvalent vaccine. The third goal leverages expertise in second generation sequencing and human genetics to study the impacts of host polymorphisms associated with immune response and resistance to malaria on vaccine efficacy. The last goal is to provide an integrative analysis of the key factors identified in the first three aims of the project to assess their impact on vaccine efficacy in multivariate analysis. This study will be the most comprehensive evaluation to date of factors, including host, parasite and environmental, that affect RTS,S effectiveness. This information will be critical for informing current large-scale rollouts of RTS,S and future malaria vaccine trials for both CS and non-CS based vaccines.